莊曜宇教授的個人資料 - Profile of Eric Y. Chuang

莊曜宇 Eric Y. Chuang

國立臺灣大學電機工程學系 教授
財團法人工業技術研究院 副總暨生醫與醫材研究所所長
國立臺灣大學與中央研究院合辦-生物資訊學國際研究生博士學位學程 教授
國立臺灣大學生醫電子與資訊學研究所　教授
國立臺灣大學生命科學系　教授
國立臺灣大學流行病學與預防醫學研究所　教授
國立臺灣大學生命科學院與中央研究院合辦-基因體與系統生物學學位學程　教授
國立臺灣大學腫瘤醫學研究所　教授
國立臺灣大學醫療器材研發中心　副主任
國立臺灣大學基因體暨精準醫學研究中心-生物資訊暨生物統計核心實驗室　主持人
Professor, Department of Electrical Engineering, National Taiwan University
Vice President, Industrial Technology Research Institute, Hsinchu, Taiwan
General Director, Biomedical Technology and Device Research Laboratories, Industrial Technology Research Institute, Hsinchu, Taiwan
Professor, Graduate Institute of Biomedical Electronics and Bioinformatics, National Taiwan University
Professor, Department of Life Science, National Taiwan University
Professor, Graduate Institute of Epidemiology and Preventive Medicine, National Taiwan University
Professor, Genome and Systems Biology Degree Program, College of Life Science, National Taiwan University
Professor, Graduate Institute of Oncology, National Taiwan University
Deputy Director, Research and Development Center for Medical Devices, National Taiwan University
Principal Investigator, Bioinformatics and Biostatistics Core Lab, NTU Center of Genomic and Precision Medicine

主要研究領域:

生物晶片、次世代定序、生物資訊、癌症生物、輻射生物、精準醫學、腸道菌、生醫大數據& AI

Major Research Areas:

Biochip, Next-Generation Sequencing, Bioinformatics, Cancer Biology, Radiation Biology, Precision Medicine, Microbiota

研究領域摘要:

*食道癌：
因應現今全球食道癌的發生機率持續攀升，然而食道癌患者卻因常在晚期才診斷出病症，而此時已不再適合做切除手術，因此導致治療效果普遍不佳。為增加療效，近幾年來，醫界發展出多種複合式療法，例如: 合併化學放射治療(concurrent chemoradiation therapy, CCRT)後再進行手術已用來增長食道癌病患的壽命，但此法僅有10%~40%食道癌患者有機會被完全治癒。本實驗室與台大外科部合作利用基因型微陣列晶片來檢視食道癌患者在施行CCRT反應與單核苷酸多型性(single-nucleotide polymorphism, SNP)的關連性。結果顯示兩種SNP(rs16863886及rs4954256)與CCRT的反應有密切的相關性，這結果已發表於頂尖的放射腫瘤國際期刊，並且通過美國與台灣的專利。
*肺癌：
肺癌是世界上持續高踞癌症死亡主因的前幾位。在癌細胞的發生過程中，癌症細胞內的目前治療肺癌的方式主要是透過化學療法和放射療法，但是這些治療方式皆會產生嚴重的副作用。我們團隊為了研究台灣非吸煙女性肺癌患者的新型分子靶點，從60名非吸煙肺癌患者中收集了成對的正常和腫瘤組織進行微陣列分析。從微陣列結果可以看出，SEMA3B，SEMA3G，SEMA5A，SEMA6A和SEMA6D在腫瘤組織中均顯著下調。我們團隊在semaphorin基因中，選擇SEMA6A進行進一步研究。第一、藉大量表現SEMA6A基因於肺癌細胞株中來探討這些基因於肺癌生成上的作用； 第二、利用微陣列來探討SEMA6A基因於肺癌生成的分子機轉； 第三、利用裸鼠實驗模型來進一步探討SEMA6A基因於體內功能上所扮演的角色。
除此之外，我們團隊以CL系列之肺癌細胞株結合生物資訊方式研究肺癌中micro-RNA及化療藥物對癌症可能之影響。結果顯示，在肺癌中miR-499a對Jagged 1的調控會促進放射線敏感性，因此可能可以做為肺癌醫療上的目標。此外，經過使用化療藥物Mitomycin C處理CL細胞實驗後，我們團隊提出直接證據證明，若未正確使用抗癌藥物可能反而會使癌細胞轉移，造成更嚴重的病況。此一系列肺癌相關研究也都已發表於相關的頂尖國際期刊中。
*台灣帝雉基因定序：
台灣帝雉，又稱帝雉和黑長尾雉，是台灣特有的長尾雉屬鳥類，棲息在海拔2500公尺以上中高海拔，地理分布於台灣的中、高海拔山區，是台灣的雉科鳥類中棲息於最高海拔者。過去台灣帝雉近年來因為溫室氣體效應，造成全球氣候急遽變化，逐漸減少成為瀕危物種，近年台灣對保育鳥類有較好的保護，許多地方 (含台灣中部山區的幾個國家公園)的野生帝雉族群有增加的現象，所以世界自然保護聯盟（IUCN）的紅皮書從1994年版將其定為近危物種。由於牠在鳥類種的分化與演化的特殊地位尚未被界定，牠的遺傳資源彌足珍貴，需要對其基因體有更詳盡的分析，以確立其在演化分類上的意義與價值。我們團隊利用既有之次世代定序平台進行帝雉全基因定序並達成下列五項目標：1.建立非模式物種定序演算平台；2.定序帝雉基因組序列；3.定序轉錄體協助基因組序列組裝；4.藉由轉錄體定序結果分析帝雉演化過程與親源；5.藉由比對其他雉科鳥類基因體以提供保育與繁殖參考。

我所指導的研究團隊長期致力於應用研究，尤其是生物晶片的開發與癌症、心臟疾病等基因體研究，利用高通量分析與資料分析方法，除了探討癌症內基因調控機制外，我們團隊亦提出了能夠準確預測各癌症預後的生物標記，這些應用研究之成果對於人類的健康與醫療具有極大貢獻，相關成果已發表在逾百篇之國際期刊論文中。以下分別說明：
*急性骨髓性白血病：
急性骨髓性白血病為台灣血癌中發生率最高的一種類型，在最近的研究中顯示，這種病人的白血病細胞中有許多基因的突變，與血癌的發生可能有重要關聯。在這項跨領域研究中，我們團隊利用高通量生物晶片技術，分析台大醫院約三百名血癌病患之基因表現圖譜，取得全基因表現之巨量資料，並使用生物資訊之分析方法，在數百個微小核糖核酸與幾萬個基因中，發現了在血癌中相當重要的三個微小核糖核酸（miR-9-5p、miR-155-5p與miR-203），以及另外十一個基因的表現可以預測病人的預後。該研究團隊並將這些微小核糖核酸及基因分別建構了兩套預測分數系統，未來病患在確診時，只需要測量這些微小核糖核酸及基因的表現情形並計算分數，即可快速的預測病患未來對治療的反應。此外，該研究團隊鎖定約四分之一帶有NPM1基因突變的血癌患者。此研究首度提出，該基因突變具有破壞血癌細胞中正常的「基因調控網路」之能力，更可能因此影響病患的預後，研究團隊並利用分子生物實驗與國際的血癌病患資料驗證了這個發現。這些成果不僅有助於了解血癌細胞內錯綜複雜的突變基因與基因網路，更提供未來抗血癌研究及開發新治療之可能標的。此研究的發現為未來血癌治療提供突破性的進展，更呼應了美國總統歐巴馬所提出的「精準醫學計畫（Precision Medicine Initiative）」，未來透過偵測這些分子標記，醫師得以了解每個患者的腫瘤細胞特性，安排個人化的治療方式，提高治癒率，同時有效地減低醫療資源的支出。上述研究成果已發表於國際腫瘤類期刊中排名前5%之白血病期刊（Leukemia）與前10%之腫瘤標靶（Oncotarget）等頂尖期刊，可見其研究品質深獲肯定，且經記者會發表後，受到眾多媒體報導，並刊載於本校校訊頭版，學術成果表現優異。
*心臟疾病：
心房顫動是最常見的一種心律不整，心房顫動患者發生中風的風險是一般人的五到七倍，我們與台大醫院心臟內科等多位醫師共同研究，利用新穎之全基因體掃描技術，發現引起心房顫動心律不整台灣特有之基因KCNIP1：第一型鈣調控鉀離子通道結合蛋白基因(Kv-channel interacting protein 1; KCNIP1)，並針對此基因進行功能性以及機轉的探討，第一個證實KCNIP1在心臟電生理的角色，帶有此基因拷貝數變異之個體，發生心房顫動風險為未帶有此基因拷貝數變異之個體的2倍多，未來將可應用在健康成人或病人檢驗，若檢驗出有上述基因拷貝數變異，可提早注意心律不整的症狀，並改善生活習慣，以減緩心房顫動及心律不整的發生，早期診斷、早期治療，進而減少台灣中風的發生率，減少社會的經濟與醫療成本。這項研究已刊載於國際知名的NATURE系列期刊NATURE COMMUNICATIONS上。
*華人乳癌基因資料庫：
我們與永齡健康基金會產學合作計畫「華人乳癌基因資料庫及個人化雲端諮詢平台」(執行期間：2015年5月至2017年5月) 針對東方人族群的乳癌進行研究，計畫建立華人女性的乳癌次世代定序基因資料庫及個人化雲端諮詢平台，用以協助醫師及患者進行個人化的乳癌療程將會有非常高的臨床醫療價值。此華人乳癌醫療諮詢平台可輸出提供醫護人員及病患、家屬友善的使用介面與基因檢測報告資訊，協助醫生提高乳癌個人化醫療的成功率。這項研究受到許多關注，台大研發處更因此專刊採訪我們，全文於106年1月刊登於刊物Landscope並公布於台大研發處英文版網站，供全球各界收看。
*建置生物資訊資料庫：
本人的研究主軸在生物醫學上，隨著研究問題拓展，不僅能以其他領域之方法解決遭逢之困難，並能輔以真實之實驗數據加速生物資訊演算法與生物統計方法之開發。現今而言，此二者結合之方向已成為當前研究之主流，以此方法尋找出的生物標記不僅只能發表於學術期刊上，且亦有其臨床醫學上的應用價值。我們與國際知名企業IBM及美國國家衛生總署NIH合作開發台灣第一套線上基因晶片分析系統(National Taiwan University Microarray Analysis Platforms)，此系統整合了多個基因資料庫與生物路徑資訊，讓使用者能在容易操作的圖型化介面下進行複雜的微陣列晶片之分析。此外，我們之研究團隊亦於2012年發表了一套微型核糖核酸線上分析工具(miRsystem)，使用者僅需輸入待研究之微型核糖核酸列表，系統即可自動進行分析統計分析，並輸出其下游之預測調控基因以及參與之生物路徑，此系統大幅簡化了生醫學者在研究微型核糖核酸上的困難，系統上線5年來已有來自82個國家、近54,000人次使用，該論文亦獲得超過149篇論文的引用，可見此系統已成為該研究領域之重要線上工具，並對於相關生醫研究帶來實質貢獻。
除了miRsystem之外，在 Biocondutor上的iGC and anamiR也有相當優秀的表現。
iGC: This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data.
自2015年9月上線以來，截至2017年9月15日，已累積了3087筆使用量。
anamiR: This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.
2016年10月上線，截至2017年9月15日用量為1360筆。

Research Summary:

Photo of Eric Y. Chuang

代表性著作 Selected Publication

  1. C.H. Sally Chen, T.H. Yuan, T.P. Lu, H.Y. Lee, Y.H. Chen, L.C. Lai, M.H. Tsai, Eric Y. Chuang*, C.C. Chan, “Exposure-associated DNA methylation among people exposed to multiple industrial pollutants,” Clinical Epigenetics, 16, Aug. 2024
  2. Chattopadhyay,Lee,Lee,Liu,Chen,Li,Lai,Tsai,Ni,Chiu,Lu,Chuang, “Twnbiome: a public database of the healthy Taiwanese gut microbiome,” BMC Bioinformatics, 24, Dec. 2023
  3. Chattopadhyay,Lee,Shen,Lu,Hsiao,Lin,Lai,Tsai,Lu,Chuang, “Multi-ethnic Imputation System (MI-System): A genotype imputation server for high-dimensional data,” Journal of Biomedical Informatics, 143, 104423, Jul. 2023
  4. Y.P. Hsieh, Y.M. Hung, M.H. Tsai, L.C. Lai, Eric Y. Chuang, “16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences,” Frontiers in Bioinformatics, 2, Aug. 2022
  5. Y.M. Hung, W.N. Lyu, M.L. Tsai, C. Liu, L.C. Lai, M.H. Tsai, Eric Y. Chuang, “To compare the performance of prokaryotic taxonomy classifiers using curated 16S full-length rRNA sequences,” Computers in Biology and Medicine, 145, 105416, Jun. 2022
  6. S. Shivani, C.Y. Kao, A. Chattopadhyay, J.W. Chen, L.C. Lai, W.H. Lin, T.P. Lu I.H. Huang, M.H. Tsai, C.H. Teng, J.J. Wu, Y.H. Hsieh, M.C. Wang, Eric Y. Chuang, “Uremic Toxin-Producing Bacteroides Species Prevail in the Gut Microbiota of Taiwanese CKD Patients: An Analysis Using the New Taiwan Microbiome Baseline,” Frontiers in Cellular and Infection Microbiology, 12, Apr. 2022
  7. P.S. Huang, Y.H. Tseng, C.F. Tsai, J.J. Chen, S.C. Yang, F.C. Chiu, Z.W. Chen, J.J. Hwang , Eric Y. Chuang*, Y.C. Wang, C.T. Tsai, “An Artificial Intelligence-Enabled ECG Algorithm for the Prediction and Localization of Angiography-Proven Coronary Artery Disease,” Biomedicines, 10, 394, Feb. 2022
  8. N.N. Phan, C.C. Huang, L.M. Tseng, Eric Y. Chuang, “Predicting Breast Cancer Gene Expression Signature by Applying Deep Convolutional Neural Networks From Unannotated Pathological Images,” Frontiers in Oncology, 11, Dec. 2021
  9. C.H. Lu, C.H. Wu, M.H. Tsai, L.C. Lai, Eric Y Chuang, “MutScape: an analytical toolkit for probing the mutational landscape in cancer genomics,” NAR Genomics and Bioinformatics, 3, Dec. 2021
  10. N.N. Phan, A. Chattopadhyay, T.T. Lee, H,I Yin, T.P. Lu, L.C. Lai, H.L. Hwa, M.H. Tsai, Eric Y Chuang, “High-performance deep learning pipeline predicts individuals in mixtures of DNA using sequencing data,” Briefings in Bioinformatics, 22, Nov. 2021
  11. W.T. Fang, C.H. Wu, Q.L. Sun, Z.T. Gu, L. Zhu, T. Mao, X.F. Zhang, N. Xu, T.P. Lu, M.H. Tsai, L.H. Chen, L.C. Lai, Eric Y. Chuang, “Novel Tumor-Specific Antigens for Immunotherapy Identified From Multi-omics Profiling in Thymic Carcinomas,” Frontiers in Immunology, 12, Nov. 2021
  12. C.Y. Lee, Y.F. Lee, L.C. Lai, M.H. Tsai, T.P. Lu, Eric Y. Chuang, “MiDSystem: A comprehensive online system for de novo assembly and analysis of microbial genomes,” New Biotechnology, 65, 42, Nov. 2021
  13. N.N. Phan, C.Y. Hsu, C.C. Huang, L.M. Tseng, Eric Y. Chuang, “Prediction of Breast Cancer Recurrence Using a Deep Convolutional Neural Network Without Region-of-Interest Labeling,” Frontiers in Oncology, 11, Oct. 2021
  14. C.H. Wu, C.S. Hsieh, Y.C. Chang, C.C. Huang, H.T. Yeh, M.F. Hou, Y.C. Chung, S.H. Tu, K.J. Chang, A. Chattopadhyay, L.C. Lai, T.P. Lu, Y.H. Li, M.H. Tsai, Eric Y. Chuang, “Differential whole-genome doubling and homologous recombination deficiencies across breast cancer subtypes from the Taiwanese population,” Communications Biology, 4, Sept. 2021
  15. A. Chattopadhyay, Z.H. Teoh, C.Y. Wu , J.M. J. Juang, L.C. Lai, M.H. Tsai, C.H. Wu, T.P. Lu, Eric Y. Chuang, “CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer,” Database, 2021, Jul. 2021
  16. C. Goswami, A. Chattopadhyay, Eric Y. Chuang, “Rare variants: data types and analysis strategies,” Annals of Translational Medicine, 9, 961, Jun. 2021
  17. J.M. Jimmy Juang, T.P. Lu, M.W. Su, C.W. Lin, J.H. Yang, H.W. Chu, C.H. Chen, Y.W. Hsiao, C.Y. Lee, L.M. Chiang, Q.Y. Yu, C.H. Kate Hsiao, C.Y. Julius Chen, P.E. Wu, C.H. Pai, Eric Y. Chuang*, C.Y. Shen, “Rare variants discovery by extensive whole-genome sequencing of the Han Chinese population in Taiwan: Applications to cardiovascular medicine,” Journal of Advanced Research, 30, 147, May 2021
  18. Y.M. Hung, M.H. Tsai, L.C. Lai, Eric Y. Chuang, “ATTRACTIVE – An Auto-Updating Database for Experimental Protocols in Regenerative Medicine,” IEEE Access, 9, 75202, May 2021
  19. C.H. Wu, H.T. Yeh, C.S. Hsieh, C.C. Huang, A. Chattopadhyay, Y.C. Chung, S.H. Tu, Y.H. Li, T.P. Lu, L.C. Lai, M.F. Hou, K.J. Chang, M.H. Tsai, Eric Y. Chuang, “Evolutionary Trajectories and Genomic Divergence in Localized Breast Cancers after Ipsilateral Breast Tumor Recurrence,” Cancers, 13, 1821, Apr. 2021
  20. S. Shivani, A. Chattopadhyay, Eric Y. Chuang, “Targeting the gut microbiome for non-communicable diseases: present and future,” Annals of Translational Medicine, 9, 361, Mar. 2021
  21. H.C. Lo, J.H. Hsu, L.C. Lai, M.H. Tsai, Eric Y. Chuang, “MicroRNA-107 enhances radiosensitivity by suppressing granulin in PC-3 prostate cancer cells,” Scientific Reports, 10, 1287, Sept. 2020
  22. H.C. Lo, D.S. Yu, H.W. Gao, M.H. Tsai, Eric Y. Chuang, “IL-27/IL-27RA signaling may modulate inflammation and progression of benign prostatic hyperplasia via suppressing the LPS/TLR4 pathway,” Translational Cancer Research, 9, 4618, Aug. 2020
  23. L.H. Chen, C.Y. Liao, L.C. Lai, M.H. Tsai, Eric Y. Chuang, “Semaphorin 6A Attenuates the Migration Capability of Lung Cancer Cells via the NRF2/HMOX1 Axis,” Scientific Reports, 9, 883, Sept. 2019
  24. L.C. Lai, Q.L. Sun, Y.A. Chen, Y.W. Hsiao, T.P. Lu, M.H. Tsai, L. Zhu, Eric Y. Chuang*, W.T. Fang, “Using proteomic profiling to characterize protein signatures of different thymoma subtypes,” BMC Cancer, 19, 883, Aug. 2019
  25. C.Y. Lee, A. Chattopadhyay, L.M. Chiang, J.M. Jimmy Juang, L.C. Lai, M.H. Tsai, T.P. Lu, Eric Y. Chuang, “VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases,” Database, 2019, Jul. 2019
  26. T.T. Wang, C.Y. Lee, L.C. Lai, M.H. Tsai, T.P. Lu, Eric Y. Chuang, “anamiR: integrated analysis of MicroRNA and gene expression profiling,” BMC Bioinformatics, 20, May 2019
  27. C.S. Hsieh, P.S. Huang, S.N. Chang, C.K. Wu, J.J. Hwang, E.Y. Chuang*, C.T. Tsai, “Genome-Wide Copy Number Variation Association Study of Atrial Fibrillation Related Thromboembolic Stroke,” J. Clin. Med, 8(3), 332, Mar. 2019
  28. C.Y. Shen, Y.C. Chang, L.H. Chen, W.C. Lin, Y.H. Lee, S.T. Yeh, H.K. Chen, W. Fang, C.P. Hsu, J.M. Lee, T.P. Lu, P.W. Hsiao, L.C. Lai, M.H. Tsai, E.Y. Chuang*, “The extracellular SEMA domain attenuates intracellular apoptotic signaling of semaphorin 6A in lung cancer cells,” Oncogenesis, Dec. 2018
  29. C.S. Hsieh, C.T. Tsai, Y.H. Chen, S.N. Chang, J.J. Hwang, E.Y. Chuang*, I.H. Wu, “Global Expression Profiling Identifies a Novel Hyaluronan Synthases 2 Gene in the Pathogenesis of Lower Extremity Varicose Veins,” J. Clin. Med, 7(12), 537, Dec. 2018
  30. C.Y. Lee, P.H. Hsieh, L.M. Chiang, A. Chattopadhyay, K.Y. Li, Y.F. Lee, T.P. Lu, L.C. Lai, E.C. Lin, H. Lee, S.T. Ding, M.H. Tsai, C.Y. Chen, E.Y. Chuang*, “Whole-Genome De Novo Sequencing Reveals Unique Genes that Contributed to the Adaptive Evolution of the Mikado Pheasant,” Gigascience, 7(5), May 2018
  31. T.H. Hsiao, Y.H. Chen, H.I. Chen, Y.C. Chiu, E.Y. Chuang*, Y. Chen, “Utilizing Cancer–Functional Gene set–Compound Networks to Identify Putative Drugs for Breast Cancer,” Comb Chem High T Scr, 21(2), 74, Feb. 2018
  32. Y.F. Lee, C.Y. Lee, L.C. Lai, M.H. Tsai, T.P. Lu, E.Y. Chuang*, “CellExpress: a comprehensive microarray-based cancer cell line and clinical sample gene expression analysis online system,” DATABASE-OXFORD, Jan. 2018
  33. Y.C. Chiu, L.J. Wang, T.H. Hsiao, E.Y. Chuang*, Y. Chen, “Genome-wide identification of key modulators of gene-gene interaction networks in breast cancer,” BMC Genomics, Oct. 2017
  34. Y.C. Chiu, L.J. Wang, T.P. Lu, T.H. Hsiao, E.Y. Chuang*, Y. Chen, “Differential correlation analysis of glioblastoma reveals immune ceRNA interactions predictive of patient survival,” BMC Bioinformatics, Feb. 2017
  35. G.L., M.H. Tsai, H.C. Lin, J.H. Hsiao, Y.C. Lee, T.P. Lu, J.M. Lee, C.P. Hsu, L.C. Lai, E.Y. Chuang*, “Identification of Methylation-Driven, Differentially Expressed STXBP6 as a Novel Biomarker in Lung Adenocarcinoma,” Scientific Reports, Feb. 2017
  36. Y.P. Lai, L.B. Wang, W.A. Wang, L.C. Lai, M.H. Tsai, T.P. Lu, E.Y. Chuang*, “iGC—an integrated analysis package of gene expression and copy number alteration,” BMC Bioinformatics, Jan. 2017
  37. Yu-Ching Hsu, Yu-Chiao Chiu, Wei-Yi Liu, Chia-Yang Cheng, Tzu-Hung Hsiao, Mong-Hsun Tsai, “A simple gene set-based analysis accurately predicts the synergy of drug pairs.,” BMC Systems Biology, Aug. 2016
  38. Chi-Yun Wu, E.Y. Chuang*, Tzu-Pin Lu, “Low correlation of lncRNA and target gene expression in microarray data,” Transl Cancer Res, Apr. 2016
  39. Govinda Lenka, Mong-Hsun Tsai, Jen-Hao Hsiao, Liang-Chuan Lai, E.Y. Chuang, “Overexpression of methylation-driven DCC suppresses proliferation of lung cancer cells.,” Transl Cancer Res, Apr. 2016
  40. Yi-Hsuan Chang, Yu-Chiao Chiu1, Yu-Ching Hsu, Hui-Mei Tsai, E.Y. Chuang*, Tzu-Hung Hsiao, “Applying gene set analysis to characterize the activities of immune cells in estrogen receptor positive breast cancer.,” Transl Cancer Res, Apr. 2016
  41. Wei-An Wang, Liang-Chuan Lai, Mong-Hsun Tsai, Tzu-Pin Lu, E.Y. Chuang, “Development of a prediction model for radiosensitivity using the expression values of genes and long non-coding RNAs,” Oncotarget, Mar. 2016
  42. T.H. Hsiao, Y.C. Chiu, P.Y. Hsu, T.P. Lu, L.C. Lai, M.H. Tsai, T.H. Huang, E.Y. Chuang*, Y. Chen, “Differential network analysis reveals the genome-wide landscape of estrogen receptor modulation in hormonal cancers,” Scientific Reports, Mar. 2016
  43. Chiu YC, Tsai MH, Chou WC, Liu YC, Kuo YY, Hou HA, Lu TP, Lai LC, Chen Y, Tien HF, Chuang EY*, “Prognostic significance of NPM1 mutation-modulated microRNA−mRNA regulation in acute myeloid leukemia.,” Leukemia, Feb. 2016
  44. Hsu YC, Chiu YC, Chen Y, Hsiao TH, Chuang EY*, “A gene-set approach to analyze copy number alterations in breast cancer.,” Translational Cancer Research, 4(3), 291, May 2015
  45. Hsu, FM, Cheng, JCH, Chang, YL, Lee, JM , Koong, AC, Chuang, EY*, “Circulating mRNA Profiling in Esophageal Squamous Cell Carcinoma Identifies FAM84B As A Biomarker In Predicting Pathological Response to Neoadjuvant Chemoradiation.,” Sci Rep, 5:10291, May 2015
  46. Lu TP, Hsiao CK, Lai LC, Tsai MH, Hsu CP, Lee JM, Chuang EY*, “Identification of regulatory SNPs associated with genetic modifications in lung adenocarcinoma.,” BMC Res Notes, 8:92, Mar. 2015
  47. Chang YY, Kuo WH, Hung JH, Lee CY, Lee YH, Chang YC, Lin WC, Shen CY, Huang CS, Hsieh FJ, Lai LC, Tsai MH, Chang KJ, Chuang EY*, “Deregulated microRNAs in triple-negative breast cancer revealed by deep sequencing.,” Molecular Cancer, 14:36, Feb. 2015
  48. Chiu YC, Hsiao TH, Chen Y, Chuang EY*, “Parameter optimization for constructing competing endogenous RNA regulatory network in glioblastoma multiforme and other cancers.,” BMC Genomics, 16(Suppl 4), S1, Feb. 2015
  49. Chiu Y.C., Wu C.T., T.H. Hsiao, Y.P. Lai, C.K. Hsiao, Y. Chen, E.Y. Chuang*, “Co-modulation analysis of gene regulation in breast cancer reveals complex interplay between ESR1 and ERBB2 genes.,” BMC Genomics, 16(Suppl 7), S19, 2015
  50. Chuang M, Chiu Y, Chou W, Hou H, Chuang EY, Tien H, “A 3-microRNA scoring system for prognostication in de novo acute myeloid leukemia patients.,” Leukemia, 29, 1051, Dec. 2014
  51. Lu TP, Hsu YY, Lai LC, Tsai MH, Chuang EY*, “Identification of gene expression biomarkers for predicting radiation exposure.,” Sci Rep, 4:6293, Sept. 2014
  52. Huang CC, Tu SH, Lien HH, Huang CS, Huang CJ, Lai LC, Tsai MH, Chuang EY*, “Refinement of breast cancer risk prediction with concordant leading edge subsets from prognostic gene signatures.,” Breast Cancer Res Tr, 147(2), 353, Sept. 2014
  53. Luo EC, Chang YC, Sher YP, Huang WY, Chuang LL, Chiu YC, Tsai MH, Chuang EY, Lai LC, “MicroRNA-769-3p down-regulates NDRG1 and enhances apoptosis in MCF-7 cells during reoxygenation.,” Sci Rep, 4:5908, Aug. 2014
  54. Wei SC, Tan YY, Weng MT, Lai LC, Hsiao JH, Chuang EY, Shun CT, Wu DC, Kao AW, Chuang CS, Ni YH, Shieh MJ, Tung CC, Chen Y, Wang CY, Xavier RJ, Podolsky DK, Wong JM, “SLCO3A1, a Novel Crohn's Disease-Associated Gene, Regulates NF-κB Activity and Associates with Intestinal Perforation.,” PLoS One, 9(6), e100515, Jun. 2014
  55. Sher YP, Wang LJ, Chuang LL, Tsai MH, Kuo TT, Huang CC, Chuang EY, Lai LC, “ADAM9 Up-Regulates N-Cadherin via miR-218 Suppression in Lung Adenocarcinoma Cells.,” PLoS One, 9(4, e94065, Apr. 2014
  56. Lu TP, Chen KT, Tsai MH, Kuo KT, Hsiao CK, Lai LC, Chuang EY*, “Identification of genes with consistent methylation levels across different human tissues.,” Sci Rep, 4:4351, Mar. 2014
  57. Lai LC, Tsai MH, Chen PC, Chen LH, Hsiao JH, Chen SK, Lu TP, Lee JM, Hsu CP, Hsiao CK, Chuang EY*, “SNP rs10248565 in HDAC9 as a novel genomic aberration biomarker of lung adenocarcinoma in non-smoking women.,” J Biomed Sci, 21:24, Mar. 2014
  58. Huang CC, Tu SH, Lien HH, Jeng JY, Liu JS, Huang CS, Lai LC, Chuang EY*, “Estrogen receptor status prediction by gene component regression: a comparative study.,” Int J Data Min Bioi, 9(2), 149, Feb. 2014
  59. Juang JM, Lu TP, Lai LC, Hsueh CH, Liu YB, Tsai CT, Lin LY, Yu CC, Hwang JJ, Chiang FT, Yeh SS, Chen WP, Chuang EY*, Lai LP, Lin JL, “Utilizing Multiple in Silico Analyses to Identify Putative Causal SCN5A Variants in Brugada Syndrome,” Sci Rep, 4:3850, Jan. 2014
  60. Huang CC, Tu SH, Huang CS, Lien HH, Lai LC, Chuang EY*, “Multiclass prediction with partial least square regression for gene expression data: applications in breast cancer intrinsic taxonomy.,” Biomed Res Int, 2013:248648, Dec. 2013
  61. Huang CC, Tu SH, Lien HH, Jeng JY, Huang CS, Huang CJ, Lai LC, Chuang EY*, “Concurrent gene signatures for han chinese breast cancers.,” PLoS One, 8(10), e76421, Oct. 2013
  62. Lai TY, Wu SD, Tsai MH, Chuang EY, Chuang LL, Hsu LC, Lai LC, “Transcription of Tnfaip3 Is Regulated by NF-κB and p38 via C/EBPβ in Activated Macrophages.,” PLoS One, 8(9), e73153, Sept. 2013
  63. Liu YJ, Lin YF, Chen YF, Luo EC, Sher YP, Tsai MH, Chuang EY, Lai LC, “MicroRNA-449a enhances radiosensitivity in CL1-0 lung adenocarcinoma cells.,” PLoS One, 8(4), e62383, Apr. 2013
  64. Huang CC, Jeng JY, Tu SH, Lien HH, Huang CS, Lai LC, Chuang EY*, “A preliminary study of concurrent gains and losses across gene expression profiles and comparative genomic hybridization in Taiwanese breast cancer patients.,” Transl Cancer Res, 2(1), 18, Feb. 2013
  65. Chen PC, Lu TP, Chang JC, Lai LC, Tsai MH, Hsiao CK, Chuang EY*, “Concurrent analysis of copy number variation and gene expression: application in paired non- smoking female lung cancer patients.,” Int J Data Min Bioinform, 8(1), 92, 2013
  66. Kuo, W.H., Y.Y. Chang, L.C. Lai, M.H. Tsai, C.K. Hsiao, K.J. Chang, and E.Y. Chuang*, “Molecular characteristics and metastasis predictor genes of triple-negative breast cancer: a clinical study of triple-negative breast carcinomas.,” PLoS One, 7(9), e45831, Sept. 2012
  67. Huang CC, Tu SH, Lien HH, Jeng JY, Liu JS, Huang CS, Wu YY, Liu CY, Lai LC, Chuang EY*, “Prediction consistency and clinical presentations of breast cancer molecular subtypes for Han Chinese population.,” J Transl Med, 10 Suppl 1, S10, Sept. 2012
  68. Lu, T.P., C.Y. Lee, M.H. Tsai, Y.C. Chiu, C.K. Hsiao, L.C. Lai, and E.Y. Chuang*, “miRSystem: an integrated system for characterizing enriched functions and pathways of microRNA targets.,” PLoS One, 7(8), e42390, Aug. 2012
  69. Hsu, F.H., H.I. Chen, M.H. Tsai, L.C. Lai, C.C. Huang, S.H. Tu, E.Y. Chuang*, and Y. Chen, “A model-based circular binary segmentation algorithm for the analysis of array CGH data.,” BMC Res Notes, 4(1), 394, Oct. 2011
  70. Lai, L.C., Y.Y. Su, K.C. Chen, M.H. Tsai, Y.P. Sher, T.P. Lu, C.Y. Lee, and E.Y. Chuang*, “Down-Regulation of NDRG1 Promotes Migration of Cancer Cells during Reoxygenation.,” PLoS One, 6(8), e24375, Sept. 2011
  71. Lu, T.P., L.C. Lai, M.H. Tsai, P.C. Chen, C.P. Hsu, J.M. Lee, C.K. Hsiao, and E.Y. Chuang*, “Integrated analyses of copy number variations and gene expression in lung adenocarcinoma.,” PLoS One, 6(9), e24829, Sept. 2011
  72. Kuo, H.C., P.Y. Lin, T.C. Chung, C.M. Chao, L.C. Lai, M.H. Tsai, and E.Y. Chuang*, “DBCAT: database of CpG islands and analytical tools for identifying comprehensive methylation profiles in cancer cells.,” J Comput Biol, 18(8), 1013, Aug. 2011
  73. Chen, P.C., Y.C. Chen, L.C. Lai, M.H. Tsai, S.K. Chen, P.W. Yang, Y.C. Lee, C.K. Hsiao, J.M. Lee, and E.Y. Chuang*, “The Use of Germline Polymorphisms in Predicting Concurrent Chemoradiotherapy Response in Esophageal Cancer.,” Int J Radiat Oncol Biol Phys, 82(5), 1996, May 2011
  74. Hsiao, T.H., C.H. Lin, T.T. Lee, J.Y. Cheng, P.K. Wei, E.Y. Chuang*, and K. Peck, “Verifying expressed transcript variants by detecting and assembling stretches of consecutive exons.,” Nucleic Acids Res, 38(20), e187, Nov. 2010
  75. Lu, T.P., M.H. Tsai, J.M. Lee, C.P. Hsu, P.C. Chen, C.W. Lin, J.Y. Shih, P.C. Yang, C.K. Hsiao, L.C. Lai, and E.Y. Chuang*, “Identification of a novel biomarker, SEMA5A, for non-small cell lung carcinoma in nonsmoking women.,” Cancer Epidemiol Biomarkers Prev, 19(10), 2590, Oct. 2010
  76. Lu, T.P., L.C. Lai, B.I. Lin, L.H. Chen, T.H. Hsiao, H.L. Liber, J.A. Cook, J.B. Mitchell, M.H. Tsai, and E.Y. Chuang*, “Distinct signaling pathways after higher or lower doses of radiation in three closely related human lymphoblast cell lines.,” Int J Radiat Oncol Biol Phys, 76(1), 212, Jan. 2010
  77. Chen, H.I., F.H. Hsu, Y. Jiang, M.H. Tsai, P.C. Yang, P.S. Meltzer, E.Y. Chuang*, and Y. Chen, “A probe-density-based analysis method for array CGH data: simulation, normalization and centralization.,” Bioinformatics, 24(16), 1749, Aug. 2008
  78. Guo, Z., M.H. Tsai, Y.H. Shiao, L.H. Chen, M.L. Wei, X. Lv, D. Gius, J.B. Little, J.B. Mitchell, and E.Y. Chuang*, “DNA (cytosine-5)-methyltransferase 1 as a mediator of mutant p53-determined p16(ink4A) down-regulation.,” J Biomed Sci, 15(2), 163, Mar. 2008
  79. Gius, D., M.C. Funk, E.Y. Chuang, S. Feng, P.C. Huettner, L. Nguyen, C.M. Bradbury, M. Mishra, S. Gao, B.M. Buttin, D.E. Cohn, M.A. Powell, N.S. Horowitz, B.P. Whitcomb, and J.S. Rader, “Profiling microdissected epithelium and stroma to model genomic signatures for cervical carcinogenesis accommodating for covariates.,” Cancer Res, 67(15), 7113, Aug. 2007
  80. Tsai, M.H., J.A. Cook, G.V. Chandramouli, W. DeGraff, H. Yan, S. Zhao, C.N. Coleman, J.B. Mitchell, and E.Y. Chuang*, “Gene expression profiling of breast, prostate, and glioma cells following single versus fractionated doses of radiation.,” Cancer Res, 67(8), 3845, Apr. 2007
  81. Chuang, E.Y., X. Chen, M.H. Tsai, H. Yan, C.Y. Li, J.B. Mitchell, H. Nagasawa, P.F. Wilson, Y. Peng, M.M. Fitzek, J.S. Bedford, and J.B. Little, “Abnormal gene expression profiles in unaffected parents of patients with hereditary-type retinoblastoma.,” Cancer Res, 66(7), 3428, Apr. 2006
  82. Tsai, M.H., X. Chen, G.V. Chandramouli, Y. Chen, H. Yan, S. Zhao, P. Keng, H.L. Liber, C.N. Coleman, J.B. Mitchell, and E.Y. Chuang*, “Transcriptional responses to ionizing radiation reveal that p53R2 protects against radiation-induced mutagenesis in human lymphoblastoid cells.,” Oncogene, 25(4), 622, Jan. 2006
  83. Tsai, M.H., H. Yan, X. Chen, G.V. Chandramouli, S. Zhao, D. Coffin, C.N. Coleman, J.B. Mitchell, and E.Y. Chuang*, “Evaluation of hybridization conditions for spotted oligonucleotide-based DNA microarrays.,” Mol Biotechnol, 29(3), 221, Mar. 2005
  84. Samuni, A.M., U. Kasid, E.Y. Chuang, S. Suy, W. Degraff, M.C. Krishna, A. Russo, and J.B. Mitchell, “Effects of hypoxia on radiation-responsive stress-activated protein kinase, p53, and caspase 3 signals in TK6 human lymphoblastoid cells.,” Cancer Res, 65(2), 579, Jan. 2005
  85. Su, H., N. Hu, J. Shih, Y. Hu, Q.H. Wang, E.Y. Chuang, M.J. Roth, C. Wang, A.M. Goldstein, T. Ding, S.M. Dawsey, C. Giffen, M.R. Emmert-Buck, and P.R. Taylor, “Gene expression analysis of esophageal squamous cell carcinoma reveals consistent molecular profiles related to a family history of upper gastrointestinal cancer.,” Cancer Res, 63(14), 3872, Jul. 2003
  86. Chuang, Y.Y., Y. Chen, Gadisetti, V.R. Chandramouli, J.A. Cook, D. Coffin, M.H. Tsai, W. DeGraff, H. Yan, S. Zhao, A. Russo, E.T. Liu, and J.B. Mitchell, “Gene expression after treatment with hydrogen peroxide, menadione, or t-butyl hydroperoxide in breast cancer cells.,” Cancer Res, 62(21), 6246, Nov. 2002
  87. Chuang, Y.Y., Q. Chen, J.P. Brown, J.M. Sedivy, and H.L. Liber, “Radiation-induced mutations at the autosomal thymidine kinase locus are not elevated in p53-null cells.,” Cancer Res, 59(13), 3073, Jul. 1999